Visualizing Salmon Population Trends with Time Series and Seasonplots

Coho, Jack Coho, and Steelhead in the Columbia River Basin

NOAA’s Historic Fisheries Collection Location: Oregon, Oregon City.

Overview

The Columbia River Basin watershed is home to several species of salmonids, inlcuding Sockeye, Coho, Jack Coho, Steelhead, and Wild Steelhead. Columbia River DART (Data Access in Real Time) provides comprehensive population and environmental data for 10 species in multiple survey locations in the basin over the last 100 years. In this report, we utilize the DART data to visualize population and adult passage trends for Coho, Jack Coho, and Steelhead across the Willamette Falls fish ladder.

Location

Map of the Willammette River basin in Oregon, including Willammette Falls fish ladder site. Source: R. Kirk Schroeder (Canadian Science Publishing)
# Read in data
fish_raw <- read_csv("willamette_fish_passage.csv")
# Make a subset with coho, steelhead, jack coho

fish_sub <- fish_raw %>% 
  clean_names() %>% 
  select(project, date, coho, jack_coho, steelhead) 

# Create time series
fish_ts <- fish_sub %>% 
  mutate(date = mdy(date)) %>% 
  as_tsibble(key = NULL, index = date)

Data Citation

Columbia River Basin DART Adult Passage Graphics & Text | Columbia Basin Research. http://www.cbr.washington.edu/dart/query/adult_graph_text.

Visualizations

Time Series

Time Series of Coho, Jack Coho, and Steelhead at Willamette Falls

# Tab 1 - time series graph

# Replace na values with 0
fish_ts_na <- fish_ts %>% 
  replace(is.na(.), 0)

# Create ts graph, but in separate panels
ts_coho <- ggplot(data = fish_ts_na) +
  geom_line(aes(x = date, y = coho), color = "deeppink2") +
  labs(y = "Coho Count", x = "Year") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 90))

ts_steelhead <- ggplot(data = fish_ts_na) +
  geom_line(aes(x = date, y = steelhead), color = "goldenrod") +
  labs(y = "Steelhead Count", x = "Year") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 90))

ts_jack_coho <- ggplot(data = fish_ts_na) +
  geom_line(aes(x = date, y = jack_coho), color = "blue2") +
  labs(y = "Jack Coho Count", x = "Year") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 90))

library(patchwork)

ts_coho | ts_steelhead | ts_jack_coho

Figure 1. Shows visual counts of Coho (pink),Steelhead (golden), and Jack Coho (blue) in adult passages in the Willamette Falls Columbia River DART survey location. Observations were taken daily from 2001 to 2010. Data source: Columbia Basin Research.

Time Series Takeaways

Seasonplots

Daily Counts of Coho, Jack Coho, and Steelhead at Willamette Falls

# Create Seasonplot showing value (counts) for each day over entire span of data, store as object
final <- annual_fish %>% 
  gg_season(y = value) +  
  facet_wrap(~species, ncol = 1, scales = "free") %>% 
  labs(x = "Month", y = "Counts") +
  theme_minimal()

final

Figure 2. shows visual counts of Coho, Jack Coho, and Steelhead in adult passages in the Willamette Falls Columbia River DART survey location. Observations were taken daily from 2001 to 2010. Data source: Columbia Basin Research.

Seasonplots Takeaways

Annual counts

Willamette Falls Annual Salmonoid Counts

annual_fish <- fish_ts %>%
  mutate(year = year(date)) %>% 
pivot_longer(`coho`:`steelhead`,
               names_to = "species",
               values_to = "value") %>% 
  group_by(species) %>% 
index_by(year) %>% 
summarize(total = sum(value, na.rm = TRUE))

# Now let's plot this!
ggplot(data = annual_fish, aes(x = year, y = total, color = species)) + 
  geom_line() +
 scale_color_manual(values=c("deeppink2", "blue2", "goldenrod")) +
  geom_point(size = 2,
             alpha = 0.8) +
  scale_x_continuous(breaks = c(2000, 2002, 2004, 2006, 2008, 2010)) +
  labs( x = "Year",
        y = "Annual Fish Observations",
        color = "Species") +
  theme_minimal()

Figure 3. Shows counts of Coho (pink),Steelhead (golden), and Jack Coho (blue), totaled annually, from the Willamette Falls observation site. Data source: Columbia Basin Research.